Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses

Yīmíng Bào, Gaya K. Amarasinghe, Christopher F. Basler, Sina Bavari, Alexander Bukreyev, Kartik Chandran, Olga Dolnik, John M. Dye, Hideki Ebihara, Pierre Formenty, Roger Hewson, Gary P. Kobinger, Eric M. Leroy, Elke Mühlberger, Sergey V. Netesov, Jean L. Patterson, Janusz T. Paweska, Sophie J. Smither, Ayato Takada, Jonathan S. TownerViktor E. Volchkov, Victoria Wahl-Jensen, Jens H. Kuhn

    Research output: Contribution to journalLetter

    7 Citations (Scopus)

    Abstract

    The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.

    Original languageEnglish (US)
    Article number106
    JournalViruses
    Volume9
    Issue number5
    DOIs
    StatePublished - May 11 2017

    Fingerprint

    Genome
    Filoviridae
    Software Design
    Information Centers
    Nucleic Acid Databases
    Biotechnology
    Virion
    Viruses

    Keywords

    • Cuevavirus
    • Ebola
    • Ebolavirus
    • Filoviridae
    • Filovirus
    • ICTV
    • Marburgvirus
    • Mononegavirales
    • Virus classification
    • Virus taxonomy

    ASJC Scopus subject areas

    • Infectious Diseases
    • Virology

    Cite this

    Bào, Y., Amarasinghe, G. K., Basler, C. F., Bavari, S., Bukreyev, A., Chandran, K., ... Kuhn, J. H. (2017). Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses. Viruses, 9(5), [106]. https://doi.org/10.3390/v9050106

    Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses. / Bào, Yīmíng; Amarasinghe, Gaya K.; Basler, Christopher F.; Bavari, Sina; Bukreyev, Alexander; Chandran, Kartik; Dolnik, Olga; Dye, John M.; Ebihara, Hideki; Formenty, Pierre; Hewson, Roger; Kobinger, Gary P.; Leroy, Eric M.; Mühlberger, Elke; Netesov, Sergey V.; Patterson, Jean L.; Paweska, Janusz T.; Smither, Sophie J.; Takada, Ayato; Towner, Jonathan S.; Volchkov, Viktor E.; Wahl-Jensen, Victoria; Kuhn, Jens H.

    In: Viruses, Vol. 9, No. 5, 106, 11.05.2017.

    Research output: Contribution to journalLetter

    Bào, Y, Amarasinghe, GK, Basler, CF, Bavari, S, Bukreyev, A, Chandran, K, Dolnik, O, Dye, JM, Ebihara, H, Formenty, P, Hewson, R, Kobinger, GP, Leroy, EM, Mühlberger, E, Netesov, SV, Patterson, JL, Paweska, JT, Smither, SJ, Takada, A, Towner, JS, Volchkov, VE, Wahl-Jensen, V & Kuhn, JH 2017, 'Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses', Viruses, vol. 9, no. 5, 106. https://doi.org/10.3390/v9050106
    Bào, Yīmíng ; Amarasinghe, Gaya K. ; Basler, Christopher F. ; Bavari, Sina ; Bukreyev, Alexander ; Chandran, Kartik ; Dolnik, Olga ; Dye, John M. ; Ebihara, Hideki ; Formenty, Pierre ; Hewson, Roger ; Kobinger, Gary P. ; Leroy, Eric M. ; Mühlberger, Elke ; Netesov, Sergey V. ; Patterson, Jean L. ; Paweska, Janusz T. ; Smither, Sophie J. ; Takada, Ayato ; Towner, Jonathan S. ; Volchkov, Viktor E. ; Wahl-Jensen, Victoria ; Kuhn, Jens H. / Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses. In: Viruses. 2017 ; Vol. 9, No. 5.
    @article{2729e582eddc4953a3e3abcf67fa301b,
    title = "Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses",
    abstract = "The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50{\%} for genera, ≈30{\%} for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58{\%} sequence diversity threshold range for genera and at the 23-36{\%} sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.",
    keywords = "Cuevavirus, Ebola, Ebolavirus, Filoviridae, Filovirus, ICTV, Marburgvirus, Mononegavirales, Virus classification, Virus taxonomy",
    author = "Yīm{\'i}ng B{\`a}o and Amarasinghe, {Gaya K.} and Basler, {Christopher F.} and Sina Bavari and Alexander Bukreyev and Kartik Chandran and Olga Dolnik and Dye, {John M.} and Hideki Ebihara and Pierre Formenty and Roger Hewson and Kobinger, {Gary P.} and Leroy, {Eric M.} and Elke M{\"u}hlberger and Netesov, {Sergey V.} and Patterson, {Jean L.} and Paweska, {Janusz T.} and Smither, {Sophie J.} and Ayato Takada and Towner, {Jonathan S.} and Volchkov, {Viktor E.} and Victoria Wahl-Jensen and Kuhn, {Jens H.}",
    year = "2017",
    month = "5",
    day = "11",
    doi = "10.3390/v9050106",
    language = "English (US)",
    volume = "9",
    journal = "Viruses",
    issn = "1999-4915",
    publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",
    number = "5",

    }

    TY - JOUR

    T1 - Implementation of objective PASC-derived taxon demarcation criteria for official classification of filoviruses

    AU - Bào, Yīmíng

    AU - Amarasinghe, Gaya K.

    AU - Basler, Christopher F.

    AU - Bavari, Sina

    AU - Bukreyev, Alexander

    AU - Chandran, Kartik

    AU - Dolnik, Olga

    AU - Dye, John M.

    AU - Ebihara, Hideki

    AU - Formenty, Pierre

    AU - Hewson, Roger

    AU - Kobinger, Gary P.

    AU - Leroy, Eric M.

    AU - Mühlberger, Elke

    AU - Netesov, Sergey V.

    AU - Patterson, Jean L.

    AU - Paweska, Janusz T.

    AU - Smither, Sophie J.

    AU - Takada, Ayato

    AU - Towner, Jonathan S.

    AU - Volchkov, Viktor E.

    AU - Wahl-Jensen, Victoria

    AU - Kuhn, Jens H.

    PY - 2017/5/11

    Y1 - 2017/5/11

    N2 - The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.

    AB - The mononegaviral family Filoviridae has eight members assigned to three genera and seven species. Until now, genus and species demarcation were based on arbitrarily chosen filovirus genome sequence divergence values (≈50% for genera, ≈30% for species) and arbitrarily chosen phenotypic virus or virion characteristics. Here we report filovirus genome sequence-based taxon demarcation criteria using the publicly accessible PAirwise Sequencing Comparison (PASC) tool of the US National Center for Biotechnology Information (Bethesda, MD, USA). Comparison of all available filovirus genomes in GenBank using PASC revealed optimal genus demarcation at the 55-58% sequence diversity threshold range for genera and at the 23-36% sequence diversity threshold range for species. Because these thresholds do not change the current official filovirus classification, these values are now implemented as filovirus taxon demarcation criteria that may solely be used for filovirus classification in case additional data are absent. A near-complete, coding-complete, or complete filovirus genome sequence will now be required to allow official classification of any novel “filovirus.” Classification of filoviruses into existing taxa or determining the need for novel taxa is now straightforward and could even become automated using a presented algorithm/flowchart rooted in RefSeq (type) sequences.

    KW - Cuevavirus

    KW - Ebola

    KW - Ebolavirus

    KW - Filoviridae

    KW - Filovirus

    KW - ICTV

    KW - Marburgvirus

    KW - Mononegavirales

    KW - Virus classification

    KW - Virus taxonomy

    UR - http://www.scopus.com/inward/record.url?scp=85019189029&partnerID=8YFLogxK

    UR - http://www.scopus.com/inward/citedby.url?scp=85019189029&partnerID=8YFLogxK

    U2 - 10.3390/v9050106

    DO - 10.3390/v9050106

    M3 - Letter

    C2 - 28492506

    AN - SCOPUS:85019189029

    VL - 9

    JO - Viruses

    JF - Viruses

    SN - 1999-4915

    IS - 5

    M1 - 106

    ER -